makeParams: Creates a parameter object of arguments to be used with other...
In BEAT: BEAT - BS-Seq Epimutation Analysis Toolkit

Description Usage Arguments Value Author(s) Examples

View source: R/BEAT.R

Creates a parameter object of arguments to be used with other BEAT functions.

makeParams(localpath = getwd(), sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)

`localpath`	Full path to working directory from which files are read and where results are saved.
`sampNames`	Vector of sample names to be analyzed.
`convrates`	Vector of empirically determined bisulfite conversion rates per sample. Determines p+, the model parameter for incomplete conversion (false negative rates).
`is.reference`	Vector of reference (TRUE) vs. single-cell (FALSE) status per sample.
`pminus`	Model parameter for false conversion (false positive rate).
`regionSize`	Region size in nucleotides into which genomic sites are grouped.
`minCounts`	Minimum counts necessary for each region to be included in epimutation modeling and analysis.
`verbose`	Shows more verbose console output during computation steps.
`computeRegions`	If set to TRUE, regions will be recomputed from individual positions and saved as cpgregions.RData objects for each sample.
`computeMatrices`	If set to TRUE, model parameters will be recomputed and saved as results.RData objects for each sample.
`writeEpicallMatrix`	If set to TRUE, epimutation calls will be written as RData object.

The function makeParams returns :

params

Parameter object to be used in other BEAT functions.

Kemal Akman <akmank@mpipz.mpg.de>

# Local working directory
localpath <- system.file('extdata', package = 'BEAT')
# Names of samples, expected filenames are e.g. reference.positions.csv
sampNames <- c("reference", "sample")
# Empirical BS-conversion rates, e.g. estimated from non-CpG methylation
convrates <- c(0.8,0.5)
# Vector denoting reference vs. single-cell status of given samples
is.reference <- c(TRUE,FALSE)
params <- makeParams(localpath, sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)
# Example usage of the params object
positions_to_regions(params)